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For Dummies® Bonus Material
By: Jean-Michel Claverie Ph.D., Cedric Notredame Ph.D.

[Bio FD Home][Ch.1][Ch.2][Ch.3][Ch.4][Ch.5][Ch.6][Ch.7][Ch.8][Ch.9][Ch.10][Ch.11][Ch.12][Ch.13][Ch.15]

Chapter 10: Editing and Publishing Alignments

Chapter 10 images

Sequence text conversion on the Web

Name	URL	Description
FMTSEQ	tofu.tamu.edu/Pise/5.a/fmtseq.html bioweb.pasteur.fr/seqanal/interfaces/fmtseq-simple.html www.bimcore.emory.edu/Pise/	Converts almost every format, including ALN (the ClustalW format); sometimes modifies sequence names
READSEQ	analysis.molbiol.ox.ac.uk/pise_html/readseq.html dot.imgen.bcm.tmc.edu/seq-util/readseq.html bio.indiana.edu/bioweb/seqanal/interfaces/readseq.html bimas.dcrt.nih.gov/molbio/readseq/ www.ebi.ac.uk/readseq/index.html	A very popular tool for reformatting; does not recognize ALN
SEQCHECK	www.swbic.org/products/bioinfo/seqcheck/seqcheck.php	Cleans your FASTA sequences

Multiple sequence alignment editing packages

Name	URL	Description
Jalview	www.ebi.ac.uk/clustalw/index.html www.es.embnet.org/Doc/jalview/help.html www.ebi.ac.uk/~michele/jalview/download.html	On the EBI server, Jalview access is offered after running ClustalW. A very complete package in Java, available online.
CINEMA	www.bioinf.man.ac.uk/dbbrowser/CINEMA2.1/	Another complete package in Java. Needs to be installed locally; runs on most platforms.
Seaview	pbil.univ-lyon1.fr/software/seaview.html	A very complete X-Window editor; very easy to install on a PC and very easy to interface with multiple sequence alignment programs.
Belvu	www.cgr.ki.se/cgr/groups/sonnhammer/Belvu.html	Very convenient for removing redundancy; supports the Selex format.
Bioedit	www.mbio.ncsu.edu/BioEdit/bioedit.html	Useful for editing RNA sequences; interfaces with BLAST.
DCSE	rrna.uia.ac.be/dcse/	Can indicate secondary structures when editing RNA.
Review	bioweb.pasteur.fr/cgi-bin/seqanal/review-edital.pl	A very complete (maybe exhaustive!) comparison of multiple sequence alignment editors.

Extracting information from a multiple sequence alignment

Name	URL	Description
Logo	www-lmmb.ncifcrf.gov/~toms/sequencelogo.html www.cbs.dtu.dk/~gorodkin/appl/plogo.html	Logos
Blocks	blocks.fhcrc.org/blocks/process_blocks.html	Identifies blocks in your multiple alignment
Blockgap	www.bork.embl-heidelberg.de/Alignment/blockgap.html	Measures blocks in your multiple alignment
Lama	blocks.fhcrc.org/blocks-bin/LAMA_search.sh	Lets you compare your multiple alignment with the BLOCKS database
Amas	www.compbio.dundee.ac.uk/servers/amas_server.html	Helps you identify features in your multiple alignment

Multiple alignment beautifying tools

Name	URL	Description
ESPript	prodes.toulouse.inra.fr/ESPript/cgi-bin/nph-ESPript_exe.cgi	Shading and coloring
Boxshade	www.ch.embnet.org/software/BOX_form.html	Shading in black and white
Mview	bioweb.pasteur.fr/seqanal/interfaces/mview_blast-simple.html	Can process BLAST alignments


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